Starting phenix.real_space_refine on Fri Aug 7 00:10:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12bj_76280/08_2026/12bj_76280.cif Found real_map, /net/cci-nas-00/data/ceres_data/12bj_76280/08_2026/12bj_76280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/12bj_76280/08_2026/12bj_76280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12bj_76280/08_2026/12bj_76280.map" model { file = "/net/cci-nas-00/data/ceres_data/12bj_76280/08_2026/12bj_76280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12bj_76280/08_2026/12bj_76280.cif" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 11205 2.51 5 N 3021 2.21 5 O 3284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17592 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2992 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 375} Chain breaks: 1 Chain: "A" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2848 Classifications: {'peptide': 382} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2955 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 371} Chain: "C" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 2989 Classifications: {'peptide': 400} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 375} Chain: "F" Number of atoms: 2853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2853 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 360} Chain breaks: 1 Chain: "D" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 2955 Classifications: {'peptide': 396} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 371} Time building chain proxies: 4.60, per 1000 atoms: 0.26 Number of scatterers: 17592 At special positions: 0 Unit cell: (123.91, 106.936, 180.773, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 3284 8.00 N 3021 7.00 C 11205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 795.2 milliseconds 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4274 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 33 sheets defined 41.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'E' and resid 13 through 24 Processing helix chain 'E' and resid 27 through 36 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 72 through 82 Processing helix chain 'E' and resid 86 through 109 Processing helix chain 'E' and resid 122 through 139 removed outlier: 3.685A pdb=" N ILE E 126 " --> pdb=" O ALA E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 190 through 201 Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 262 through 273 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 302 through 314 Processing helix chain 'E' and resid 364 through 376 removed outlier: 3.641A pdb=" N CYS E 368 " --> pdb=" O GLU E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 395 removed outlier: 3.504A pdb=" N VAL E 382 " --> pdb=" O PRO E 378 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA E 395 " --> pdb=" O ARG E 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.633A pdb=" N GLY A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.616A pdb=" N SER A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 122 through 139 removed outlier: 3.846A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 262 through 273 Processing helix chain 'A' and resid 285 through 289 removed outlier: 3.558A pdb=" N GLY A 288 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A 289 " --> pdb=" O LYS A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 289' Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 364 through 376 Processing helix chain 'A' and resid 378 through 395 removed outlier: 4.135A pdb=" N ALA A 395 " --> pdb=" O ARG A 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 24 Processing helix chain 'B' and resid 27 through 35 Processing helix chain 'B' and resid 36 through 39 removed outlier: 3.746A pdb=" N GLY B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 36 through 39' Processing helix chain 'B' and resid 72 through 83 Processing helix chain 'B' and resid 86 through 109 Processing helix chain 'B' and resid 122 through 139 removed outlier: 4.122A pdb=" N ILE B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 262 through 273 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 364 through 376 removed outlier: 3.593A pdb=" N CYS B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 394 removed outlier: 3.533A pdb=" N VAL B 382 " --> pdb=" O PRO B 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 86 through 109 Processing helix chain 'C' and resid 122 through 139 removed outlier: 3.765A pdb=" N ILE C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 139 " --> pdb=" O GLY C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 262 through 274 removed outlier: 3.732A pdb=" N GLY C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 302 through 314 Processing helix chain 'C' and resid 364 through 376 Processing helix chain 'C' and resid 378 through 396 removed outlier: 3.625A pdb=" N VAL C 382 " --> pdb=" O PRO C 378 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE C 396 " --> pdb=" O ALA C 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 25 removed outlier: 3.778A pdb=" N GLY F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 37 removed outlier: 3.786A pdb=" N GLY F 37 " --> pdb=" O SER F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 82 removed outlier: 3.646A pdb=" N ASN F 82 " --> pdb=" O GLY F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 109 Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 122 through 139 removed outlier: 3.969A pdb=" N ILE F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 174 Processing helix chain 'F' and resid 190 through 201 Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 273 Processing helix chain 'F' and resid 285 through 289 removed outlier: 3.754A pdb=" N GLY F 288 " --> pdb=" O MET F 285 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG F 289 " --> pdb=" O LYS F 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 285 through 289' Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 302 through 313 Processing helix chain 'F' and resid 364 through 376 Processing helix chain 'F' and resid 378 through 396 Processing helix chain 'D' and resid 13 through 25 removed outlier: 3.800A pdb=" N GLY D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 72 through 82 removed outlier: 3.677A pdb=" N ASN D 82 " --> pdb=" O GLY D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 109 Processing helix chain 'D' and resid 122 through 139 removed outlier: 3.522A pdb=" N ILE D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 139 " --> pdb=" O GLY D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 190 through 201 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 262 through 273 Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 364 through 376 removed outlier: 4.110A pdb=" N CYS D 368 " --> pdb=" O GLU D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 395 removed outlier: 3.572A pdb=" N VAL D 382 " --> pdb=" O PRO D 378 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 143 through 146 removed outlier: 6.829A pdb=" N LYS E 2 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ILE E 145 " --> pdb=" O LYS E 2 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N ALA E 4 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG E 231 " --> pdb=" O ASP E 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 43 through 51 Processing sheet with id=AA3, first strand: chain 'E' and resid 149 through 151 removed outlier: 6.604A pdb=" N LEU E 149 " --> pdb=" O TYR E 180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL E 179 " --> pdb=" O MET D 210 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 154 through 158 removed outlier: 4.205A pdb=" N GLY E 154 " --> pdb=" O VAL E 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 252 through 255 removed outlier: 3.700A pdb=" N ASP E 277 " --> pdb=" O LEU E 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 252 through 255 Processing sheet with id=AA7, first strand: chain 'E' and resid 318 through 319 Processing sheet with id=AA8, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.670A pdb=" N GLN E 325 " --> pdb=" O PHE F 321 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLY F 318 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THR F 254 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 324 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 326 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU F 246 " --> pdb=" O ARG F 326 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 277 through 278 removed outlier: 3.889A pdb=" N ASP F 277 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU F 246 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG F 326 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP F 324 " --> pdb=" O SER F 248 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N THR F 254 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLY F 318 " --> pdb=" O THR F 254 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ARG F 323 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ARG D 323 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLY D 318 " --> pdb=" O THR D 254 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N THR D 254 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL D 250 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 277 " --> pdb=" O LEU D 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 330 through 338 removed outlier: 3.502A pdb=" N ALA E 334 " --> pdb=" O VAL E 345 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR E 350 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 203 through 204 removed outlier: 4.444A pdb=" N SER A 203 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 146 " --> pdb=" O SER A 203 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS A 2 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS A 143 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 231 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU A 232 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL A 215 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 234 " --> pdb=" O THR A 213 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 236 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU B 149 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 45 through 51 Processing sheet with id=AB4, first strand: chain 'A' and resid 277 through 282 removed outlier: 3.850A pdb=" N ASP A 277 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN C 325 " --> pdb=" O PHE A 321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 327 through 328 removed outlier: 10.056A pdb=" N ARG B 323 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ARG C 323 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 325 " --> pdb=" O PHE C 321 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLY C 318 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR C 254 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP B 277 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 298 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N THR B 254 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N GLY B 318 " --> pdb=" O THR B 254 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 330 through 337 removed outlier: 3.788A pdb=" N GLN A 330 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A 336 " --> pdb=" O VAL A 343 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 203 through 204 removed outlier: 4.027A pdb=" N SER B 203 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER B 146 " --> pdb=" O SER B 203 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS B 2 " --> pdb=" O LYS B 143 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ILE B 145 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA B 4 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 231 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU B 232 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL B 215 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU B 234 " --> pdb=" O THR B 213 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU B 236 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 211 " --> pdb=" O GLU B 236 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 149 " --> pdb=" O PRO C 178 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 43 through 51 removed outlier: 3.514A pdb=" N ARG B 48 " --> pdb=" O ASP B 59 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 154 through 158 removed outlier: 3.811A pdb=" N GLY B 154 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY B 161 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 330 through 338 removed outlier: 3.972A pdb=" N TYR B 350 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE B 358 " --> pdb=" O TYR B 350 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 330 through 338 Processing sheet with id=AC3, first strand: chain 'C' and resid 203 through 204 removed outlier: 4.094A pdb=" N SER C 203 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 146 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LYS C 2 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 145 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA C 4 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N MET C 1 " --> pdb=" O ILE C 237 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU C 232 " --> pdb=" O VAL C 215 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VAL C 215 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C 234 " --> pdb=" O THR C 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 43 through 51 Processing sheet with id=AC5, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AC6, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AC7, first strand: chain 'F' and resid 203 through 204 removed outlier: 4.236A pdb=" N SER F 203 " --> pdb=" O VAL F 144 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N ILE F 145 " --> pdb=" O LYS F 2 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ALA F 4 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG F 231 " --> pdb=" O ASP F 7 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 43 through 51 removed outlier: 3.559A pdb=" N ARG F 46 " --> pdb=" O ALA F 61 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 149 through 151 removed outlier: 6.474A pdb=" N LEU F 149 " --> pdb=" O TYR F 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 330 through 338 removed outlier: 3.702A pdb=" N GLN F 330 " --> pdb=" O LEU F 349 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL F 336 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL F 343 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR F 350 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE F 358 " --> pdb=" O TYR F 350 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 203 through 204 removed outlier: 4.099A pdb=" N SER D 203 " --> pdb=" O VAL D 144 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 3 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 235 " --> pdb=" O ILE D 3 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 43 through 51 Processing sheet with id=AD4, first strand: chain 'D' and resid 149 through 151 removed outlier: 6.303A pdb=" N LEU D 149 " --> pdb=" O TYR D 180 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 154 through 157 removed outlier: 4.094A pdb=" N GLY D 154 " --> pdb=" O VAL D 165 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 330 through 338 removed outlier: 3.521A pdb=" N GLN D 330 " --> pdb=" O LEU D 349 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 348 " --> pdb=" O ASN D 360 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN D 360 " --> pdb=" O GLY D 348 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR D 350 " --> pdb=" O ILE D 358 " (cutoff:3.500A) 950 hydrogen bonds defined for protein. 2739 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.38 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5858 1.34 - 1.46: 3624 1.46 - 1.58: 8337 1.58 - 1.70: 1 1.70 - 1.82: 124 Bond restraints: 17944 Sorted by residual: bond pdb=" CG PRO D 299 " pdb=" CD PRO D 299 " ideal model delta sigma weight residual 1.503 1.226 0.277 3.40e-02 8.65e+02 6.63e+01 bond pdb=" N SER E 247 " pdb=" CA SER E 247 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.29e-02 6.01e+03 7.01e+00 bond pdb=" N ASN E 238 " pdb=" CA ASN E 238 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.68e+00 bond pdb=" N PRO E 225 " pdb=" CD PRO E 225 " ideal model delta sigma weight residual 1.473 1.438 0.035 1.40e-02 5.10e+03 6.25e+00 bond pdb=" N SER E 239 " pdb=" CA SER E 239 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.17e-02 7.31e+03 6.16e+00 ... (remaining 17939 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 24300 4.10 - 8.19: 69 8.19 - 12.29: 11 12.29 - 16.38: 3 16.38 - 20.48: 2 Bond angle restraints: 24385 Sorted by residual: angle pdb=" N PRO D 299 " pdb=" CD PRO D 299 " pdb=" CG PRO D 299 " ideal model delta sigma weight residual 103.20 82.72 20.48 1.50e+00 4.44e-01 1.86e+02 angle pdb=" CA PRO D 299 " pdb=" CB PRO D 299 " pdb=" CG PRO D 299 " ideal model delta sigma weight residual 104.50 84.44 20.06 1.90e+00 2.77e-01 1.11e+02 angle pdb=" CA PRO E 225 " pdb=" N PRO E 225 " pdb=" CD PRO E 225 " ideal model delta sigma weight residual 112.00 100.03 11.97 1.40e+00 5.10e-01 7.32e+01 angle pdb=" N PRO E 225 " pdb=" CD PRO E 225 " pdb=" CG PRO E 225 " ideal model delta sigma weight residual 103.20 93.24 9.96 1.50e+00 4.44e-01 4.41e+01 angle pdb=" N PRO D 299 " pdb=" CA PRO D 299 " pdb=" CB PRO D 299 " ideal model delta sigma weight residual 103.45 95.73 7.72 1.21e+00 6.83e-01 4.07e+01 ... (remaining 24380 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 9254 17.99 - 35.97: 1212 35.97 - 53.96: 280 53.96 - 71.94: 34 71.94 - 89.93: 16 Dihedral angle restraints: 10796 sinusoidal: 4125 harmonic: 6671 Sorted by residual: dihedral pdb=" N PRO D 299 " pdb=" CG PRO D 299 " pdb=" CD PRO D 299 " pdb=" CB PRO D 299 " ideal model delta sinusoidal sigma weight residual 30.00 79.80 -49.80 1 1.50e+01 4.44e-03 1.51e+01 dihedral pdb=" N PRO E 225 " pdb=" CG PRO E 225 " pdb=" CD PRO E 225 " pdb=" CB PRO E 225 " ideal model delta sinusoidal sigma weight residual 30.00 75.32 -45.32 1 1.50e+01 4.44e-03 1.27e+01 dihedral pdb=" CB GLU C 366 " pdb=" CG GLU C 366 " pdb=" CD GLU C 366 " pdb=" OE1 GLU C 366 " ideal model delta sinusoidal sigma weight residual 0.00 89.93 -89.93 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 10793 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2123 0.039 - 0.078: 468 0.078 - 0.117: 220 0.117 - 0.156: 32 0.156 - 0.195: 2 Chirality restraints: 2845 Sorted by residual: chirality pdb=" CG LEU F 35 " pdb=" CB LEU F 35 " pdb=" CD1 LEU F 35 " pdb=" CD2 LEU F 35 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CA GLU E 245 " pdb=" N GLU E 245 " pdb=" C GLU E 245 " pdb=" CB GLU E 245 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA GLU E 246 " pdb=" N GLU E 246 " pdb=" C GLU E 246 " pdb=" CB GLU E 246 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 2842 not shown) Planarity restraints: 3175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 226 " 0.054 5.00e-02 4.00e+02 7.94e-02 1.01e+01 pdb=" N PRO A 227 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 149 " -0.052 5.00e-02 4.00e+02 7.68e-02 9.45e+00 pdb=" N PRO A 150 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO A 150 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 150 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 224 " 0.041 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO E 225 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 225 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 225 " 0.033 5.00e-02 4.00e+02 ... (remaining 3172 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 279 2.67 - 3.23: 15733 3.23 - 3.78: 25316 3.78 - 4.34: 31137 4.34 - 4.90: 54373 Nonbonded interactions: 126838 Sorted by model distance: nonbonded pdb=" OG SER F 13 " pdb=" OD1 ASP F 15 " model vdw 2.111 3.040 nonbonded pdb=" O SER E 315 " pdb=" OG SER E 315 " model vdw 2.182 3.040 nonbonded pdb=" OG SER D 13 " pdb=" OD1 ASP D 15 " model vdw 2.203 3.040 nonbonded pdb=" O SER A 315 " pdb=" OG SER A 315 " model vdw 2.219 3.040 nonbonded pdb=" OG SER A 13 " pdb=" OD1 ASP A 15 " model vdw 2.227 3.040 ... (remaining 126833 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 241 or resid 244 through 396)) selection = (chain 'B' and (resid 1 through 153 or resid 168 through 241 or resid 244 throug \ h 396)) selection = (chain 'C' and (resid 1 through 153 or resid 168 through 241 or resid 244 throug \ h 396)) selection = (chain 'D' and (resid 1 through 153 or resid 168 through 241 or resid 244 throug \ h 396)) selection = (chain 'E' and (resid 1 through 153 or resid 168 through 396)) selection = (chain 'F' and (resid 1 through 153 or resid 168 through 241 or resid 244 throug \ h 396)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.770 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.277 17944 Z= 0.152 Angle : 0.688 20.479 24385 Z= 0.349 Chirality : 0.041 0.195 2845 Planarity : 0.005 0.079 3175 Dihedral : 16.603 89.927 6522 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.01 % Favored : 97.86 % Rotamer: Outliers : 0.38 % Allowed : 30.10 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2339 helix: 2.17 (0.18), residues: 877 sheet: 0.02 (0.20), residues: 703 loop : -0.52 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 48 TYR 0.014 0.001 TYR B 340 PHE 0.014 0.001 PHE E 97 TRP 0.028 0.001 TRP A 43 HIS 0.003 0.000 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (17944) covalent geometry : angle 0.68807 / 0.35 (24385) hydrogen bonds : bond 0.20531 / 13.95 ( 921) hydrogen bonds : angle 7.55600 / 5.30 ( 2739) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7476 (t0) cc_final: 0.7093 (t0) REVERT: A 16 MET cc_start: 0.7329 (mmt) cc_final: 0.5282 (mtt) REVERT: A 258 MET cc_start: 0.7914 (ttt) cc_final: 0.7658 (ttt) REVERT: C 243 GLU cc_start: 0.7214 (pp20) cc_final: 0.7002 (pp20) REVERT: D 128 ASP cc_start: 0.7671 (p0) cc_final: 0.7446 (p0) outliers start: 7 outliers final: 2 residues processed: 189 average time/residue: 0.1120 time to fit residues: 35.5762 Evaluate side-chains 173 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain A residue 213 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 118 HIS E 228 ASN B 114 GLN F 70 HIS D 82 ASN D 108 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.166552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.126856 restraints weight = 25140.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.126339 restraints weight = 38951.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.127998 restraints weight = 32112.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.128358 restraints weight = 19381.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.131926 restraints weight = 16781.196| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17944 Z= 0.133 Angle : 0.600 13.488 24385 Z= 0.288 Chirality : 0.042 0.148 2845 Planarity : 0.005 0.053 3175 Dihedral : 3.760 53.905 2506 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.05 % Rotamer: Outliers : 3.20 % Allowed : 25.87 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2339 helix: 2.19 (0.18), residues: 896 sheet: 0.13 (0.20), residues: 704 loop : -0.74 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 48 TYR 0.010 0.001 TYR A 172 PHE 0.013 0.001 PHE E 97 TRP 0.019 0.001 TRP A 43 HIS 0.005 0.001 HIS F 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.13 (17944) covalent geometry : angle 0.60008 / 0.29 (24385) hydrogen bonds : bond 0.03767 / 2.58 ( 921) hydrogen bonds : angle 5.07506 / 3.61 ( 2739) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 202 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7476 (t0) cc_final: 0.7009 (t0) REVERT: F 31 LEU cc_start: 0.8352 (pp) cc_final: 0.8075 (tp) REVERT: F 213 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8788 (m) outliers start: 59 outliers final: 26 residues processed: 243 average time/residue: 0.1150 time to fit residues: 45.8686 Evaluate side-chains 204 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 213 THR Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 349 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 30 optimal weight: 0.9980 chunk 171 optimal weight: 0.0870 chunk 225 optimal weight: 0.6980 chunk 193 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 chunk 233 optimal weight: 10.0000 chunk 166 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN F 70 HIS D 108 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.126124 restraints weight = 25922.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123959 restraints weight = 32353.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.125534 restraints weight = 31927.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126326 restraints weight = 17344.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128151 restraints weight = 15407.793| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17944 Z= 0.110 Angle : 0.550 11.753 24385 Z= 0.263 Chirality : 0.041 0.142 2845 Planarity : 0.005 0.054 3175 Dihedral : 3.650 55.858 2505 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.05 % Favored : 97.91 % Rotamer: Outliers : 2.93 % Allowed : 25.98 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2339 helix: 2.32 (0.18), residues: 897 sheet: 0.17 (0.20), residues: 706 loop : -0.74 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 48 TYR 0.007 0.001 TYR C 180 PHE 0.013 0.001 PHE E 97 TRP 0.021 0.001 TRP A 43 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (17944) covalent geometry : angle 0.54992 / 0.26 (24385) hydrogen bonds : bond 0.03235 / 2.23 ( 921) hydrogen bonds : angle 4.58182 / 3.25 ( 2739) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 196 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7528 (t0) cc_final: 0.7080 (t0) REVERT: A 16 MET cc_start: 0.7411 (mmt) cc_final: 0.5461 (mtt) REVERT: A 271 MET cc_start: 0.8690 (mmm) cc_final: 0.8368 (tpp) REVERT: B 368 CYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8446 (m) REVERT: C 100 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8720 (tt) REVERT: F 70 HIS cc_start: 0.1451 (OUTLIER) cc_final: 0.1100 (t-170) REVERT: D 36 LYS cc_start: 0.6235 (tppt) cc_final: 0.5875 (tppt) REVERT: D 383 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.6802 (m-80) outliers start: 54 outliers final: 26 residues processed: 236 average time/residue: 0.1144 time to fit residues: 43.8104 Evaluate side-chains 204 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 24 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 131 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 148 optimal weight: 0.7980 chunk 181 optimal weight: 0.0870 chunk 191 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS C 82 ASN ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 68 GLN F 70 HIS ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 175 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.165115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123469 restraints weight = 26002.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.119704 restraints weight = 37452.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.122299 restraints weight = 32539.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.122673 restraints weight = 19142.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126415 restraints weight = 16601.068| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17944 Z= 0.181 Angle : 0.607 11.359 24385 Z= 0.296 Chirality : 0.043 0.149 2845 Planarity : 0.005 0.055 3175 Dihedral : 3.989 57.765 2505 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.33 % Favored : 96.62 % Rotamer: Outliers : 4.56 % Allowed : 25.38 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2339 helix: 2.28 (0.18), residues: 898 sheet: 0.07 (0.20), residues: 695 loop : -0.90 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 46 TYR 0.009 0.001 TYR C 180 PHE 0.018 0.002 PHE E 9 TRP 0.024 0.001 TRP A 43 HIS 0.021 0.001 HIS F 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 (17944) covalent geometry : angle 0.60696 / 0.30 (24385) hydrogen bonds : bond 0.04055 / 2.80 ( 921) hydrogen bonds : angle 4.60709 / 3.27 ( 2739) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 183 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7608 (t0) cc_final: 0.7315 (t0) REVERT: A 16 MET cc_start: 0.7639 (mmt) cc_final: 0.5924 (mtm) REVERT: A 48 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.7065 (mtp-110) REVERT: A 271 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8390 (tpp) REVERT: B 368 CYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8395 (m) REVERT: C 100 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8807 (tt) REVERT: F 226 HIS cc_start: 0.8554 (p90) cc_final: 0.8270 (p90) REVERT: D 192 THR cc_start: 0.8989 (p) cc_final: 0.8722 (t) outliers start: 84 outliers final: 51 residues processed: 254 average time/residue: 0.1092 time to fit residues: 45.8531 Evaluate side-chains 224 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 24 CYS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 300 GLU Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 310 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 119 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 178 optimal weight: 20.0000 chunk 40 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN C 108 HIS ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 106 GLN D 108 HIS D 137 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.112627 restraints weight = 26367.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110623 restraints weight = 42308.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112385 restraints weight = 34850.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.113146 restraints weight = 20088.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116144 restraints weight = 16942.313| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 17944 Z= 0.331 Angle : 0.761 10.951 24385 Z= 0.379 Chirality : 0.048 0.169 2845 Planarity : 0.006 0.055 3175 Dihedral : 4.908 62.132 2505 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.32 % Favored : 95.64 % Rotamer: Outliers : 5.91 % Allowed : 25.81 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2339 helix: 1.79 (0.18), residues: 893 sheet: -0.23 (0.20), residues: 696 loop : -1.37 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 323 TYR 0.012 0.002 TYR D 180 PHE 0.029 0.003 PHE B 262 TRP 0.025 0.002 TRP A 43 HIS 0.010 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00825 / 0.33 (17944) covalent geometry : angle 0.76105 / 0.38 (24385) hydrogen bonds : bond 0.05458 / 3.78 ( 921) hydrogen bonds : angle 5.02956 / 3.58 ( 2739) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 169 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 210 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8056 (ptp) REVERT: A 48 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7235 (mtp-110) REVERT: A 271 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8302 (ttm) REVERT: B 7 ASP cc_start: 0.8462 (t0) cc_final: 0.8215 (t0) REVERT: B 207 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8766 (t80) REVERT: D 138 LEU cc_start: 0.8344 (mt) cc_final: 0.8055 (tt) REVERT: D 207 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8447 (t80) outliers start: 109 outliers final: 72 residues processed: 260 average time/residue: 0.1139 time to fit residues: 48.6567 Evaluate side-chains 229 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 152 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 312 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 325 GLN Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 117 PHE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 310 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 64 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 228 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN B 114 GLN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN D 108 HIS D 137 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116509 restraints weight = 26056.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113836 restraints weight = 31786.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.115265 restraints weight = 33249.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116286 restraints weight = 17622.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119029 restraints weight = 15055.437| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17944 Z= 0.141 Angle : 0.604 12.377 24385 Z= 0.292 Chirality : 0.043 0.216 2845 Planarity : 0.005 0.057 3175 Dihedral : 4.274 58.828 2505 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Rotamer: Outliers : 4.77 % Allowed : 27.01 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.18), residues: 2339 helix: 2.12 (0.18), residues: 894 sheet: -0.22 (0.20), residues: 712 loop : -1.15 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.008 0.001 TYR C 180 PHE 0.014 0.001 PHE E 294 TRP 0.027 0.001 TRP A 43 HIS 0.022 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (17944) covalent geometry : angle 0.60392 / 0.29 (24385) hydrogen bonds : bond 0.03603 / 2.48 ( 921) hydrogen bonds : angle 4.52718 / 3.23 ( 2739) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 169 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7537 (t0) cc_final: 0.7045 (t0) REVERT: E 210 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8149 (ptm) REVERT: A 16 MET cc_start: 0.7783 (mmt) cc_final: 0.6801 (mtm) REVERT: A 48 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7178 (mtp-110) REVERT: A 271 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8146 (ttm) REVERT: B 7 ASP cc_start: 0.8356 (t0) cc_final: 0.8109 (t0) REVERT: C 100 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8795 (tt) REVERT: F 70 HIS cc_start: 0.3801 (t70) cc_final: 0.2836 (t-170) REVERT: F 97 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: F 271 MET cc_start: 0.8654 (mmm) cc_final: 0.8446 (mmm) outliers start: 88 outliers final: 56 residues processed: 248 average time/residue: 0.1078 time to fit residues: 44.6530 Evaluate side-chains 217 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 156 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 17 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 17 CYS Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain B residue 370 GLN Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 310 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 70 optimal weight: 0.7980 chunk 129 optimal weight: 0.0980 chunk 218 optimal weight: 0.9990 chunk 17 optimal weight: 0.0770 chunk 131 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 ASN ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.160877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.117603 restraints weight = 26188.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114754 restraints weight = 30834.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.116287 restraints weight = 33019.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.117149 restraints weight = 17770.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121006 restraints weight = 15432.146| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17944 Z= 0.104 Angle : 0.574 12.933 24385 Z= 0.273 Chirality : 0.041 0.142 2845 Planarity : 0.005 0.057 3175 Dihedral : 3.959 57.162 2505 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Rotamer: Outliers : 3.52 % Allowed : 28.42 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2339 helix: 2.23 (0.18), residues: 897 sheet: -0.02 (0.20), residues: 688 loop : -0.96 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 323 TYR 0.008 0.001 TYR C 180 PHE 0.016 0.001 PHE A 97 TRP 0.031 0.001 TRP A 43 HIS 0.025 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (17944) covalent geometry : angle 0.57449 / 0.27 (24385) hydrogen bonds : bond 0.03022 / 2.08 ( 921) hydrogen bonds : angle 4.30596 / 3.07 ( 2739) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 159 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7470 (t0) cc_final: 0.6974 (t0) REVERT: A 16 MET cc_start: 0.7645 (mmt) cc_final: 0.6780 (mtp) REVERT: A 48 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7234 (mtp-110) REVERT: A 55 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.7987 (tp) REVERT: A 271 MET cc_start: 0.8754 (mmm) cc_final: 0.7990 (ttm) REVERT: C 100 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8709 (tt) REVERT: F 70 HIS cc_start: 0.3621 (t70) cc_final: 0.2626 (t-170) REVERT: F 97 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: F 226 HIS cc_start: 0.8597 (p90) cc_final: 0.8239 (p90) REVERT: F 231 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7386 (ttp-110) REVERT: D 106 GLN cc_start: 0.8614 (tp40) cc_final: 0.8391 (tt0) REVERT: D 383 TYR cc_start: 0.7099 (OUTLIER) cc_final: 0.6423 (t80) outliers start: 65 outliers final: 44 residues processed: 214 average time/residue: 0.1050 time to fit residues: 37.4463 Evaluate side-chains 202 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 203 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 300 GLU Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 196 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117003 restraints weight = 26165.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.115874 restraints weight = 41010.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117487 restraints weight = 33858.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118238 restraints weight = 19869.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.121086 restraints weight = 16843.830| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17944 Z= 0.162 Angle : 0.609 12.537 24385 Z= 0.294 Chirality : 0.042 0.147 2845 Planarity : 0.005 0.058 3175 Dihedral : 4.023 57.867 2505 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.90 % Allowed : 28.15 % Favored : 67.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.18), residues: 2339 helix: 2.25 (0.18), residues: 894 sheet: -0.07 (0.20), residues: 708 loop : -0.97 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.010 0.001 TYR A 177 PHE 0.017 0.002 PHE D 280 TRP 0.030 0.001 TRP A 43 HIS 0.028 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 (17944) covalent geometry : angle 0.60913 / 0.29 (24385) hydrogen bonds : bond 0.03741 / 2.59 ( 921) hydrogen bonds : angle 4.41481 / 3.14 ( 2739) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 156 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7504 (t0) cc_final: 0.7165 (t0) REVERT: A 16 MET cc_start: 0.7521 (mmt) cc_final: 0.6903 (mtp) REVERT: A 48 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7252 (mtp-110) REVERT: A 271 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: B 7 ASP cc_start: 0.8364 (t0) cc_final: 0.8104 (t0) REVERT: B 207 PHE cc_start: 0.9049 (OUTLIER) cc_final: 0.8752 (t80) REVERT: C 100 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8799 (tt) REVERT: C 326 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7878 (mtp85) REVERT: F 70 HIS cc_start: 0.3742 (t70) cc_final: 0.2729 (t-170) REVERT: F 97 PHE cc_start: 0.7502 (OUTLIER) cc_final: 0.7175 (m-80) REVERT: F 226 HIS cc_start: 0.8588 (p90) cc_final: 0.8247 (p90) REVERT: F 231 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7490 (ttp-110) REVERT: D 106 GLN cc_start: 0.8609 (tp40) cc_final: 0.8399 (tt0) REVERT: D 383 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6717 (t80) outliers start: 72 outliers final: 54 residues processed: 217 average time/residue: 0.1081 time to fit residues: 38.6932 Evaluate side-chains 215 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 153 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 383 TYR Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 48 ARG Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 54 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 198 optimal weight: 8.9990 chunk 156 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.159339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.116840 restraints weight = 26234.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.113510 restraints weight = 29722.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.114807 restraints weight = 33570.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116033 restraints weight = 17784.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.118442 restraints weight = 14937.651| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17944 Z= 0.130 Angle : 0.586 12.411 24385 Z= 0.280 Chirality : 0.042 0.151 2845 Planarity : 0.005 0.058 3175 Dihedral : 3.862 56.344 2505 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.69 % Allowed : 28.15 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.18), residues: 2339 helix: 2.28 (0.18), residues: 895 sheet: -0.05 (0.20), residues: 711 loop : -0.93 (0.21), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 323 TYR 0.009 0.001 TYR A 177 PHE 0.015 0.001 PHE E 97 TRP 0.033 0.001 TRP A 43 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (17944) covalent geometry : angle 0.58587 / 0.28 (24385) hydrogen bonds : bond 0.03315 / 2.29 ( 921) hydrogen bonds : angle 4.32470 / 3.08 ( 2739) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 154 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7473 (t0) cc_final: 0.7145 (t0) REVERT: A 16 MET cc_start: 0.7597 (mmt) cc_final: 0.7050 (mtp) REVERT: A 55 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8018 (tp) REVERT: A 271 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8024 (ttm) REVERT: B 207 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.8700 (t80) REVERT: C 100 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8695 (tt) REVERT: C 326 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7813 (mtp85) REVERT: F 70 HIS cc_start: 0.3670 (t70) cc_final: 0.2674 (t-170) REVERT: F 97 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7468 (m-80) REVERT: F 226 HIS cc_start: 0.8619 (p90) cc_final: 0.8332 (p90) REVERT: F 231 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7310 (ttp-110) REVERT: D 106 GLN cc_start: 0.8731 (tp40) cc_final: 0.8486 (tt0) REVERT: D 383 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6502 (t80) outliers start: 68 outliers final: 53 residues processed: 210 average time/residue: 0.0990 time to fit residues: 34.6190 Evaluate side-chains 212 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 151 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain F residue 383 TYR Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 97 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 219 optimal weight: 6.9990 chunk 217 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 185 optimal weight: 0.5980 chunk 216 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 137 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.161188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118257 restraints weight = 26025.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113763 restraints weight = 32267.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116268 restraints weight = 33315.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.116736 restraints weight = 18756.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.119659 restraints weight = 16732.011| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17944 Z= 0.103 Angle : 0.571 13.398 24385 Z= 0.269 Chirality : 0.041 0.162 2845 Planarity : 0.005 0.059 3175 Dihedral : 3.673 54.768 2505 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.93 % Allowed : 29.01 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 2339 helix: 2.32 (0.18), residues: 896 sheet: 0.07 (0.20), residues: 705 loop : -0.85 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.009 0.001 TYR A 177 PHE 0.014 0.001 PHE E 97 TRP 0.034 0.001 TRP A 43 HIS 0.010 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (17944) covalent geometry : angle 0.57051 / 0.27 (24385) hydrogen bonds : bond 0.02945 / 2.03 ( 921) hydrogen bonds : angle 4.22790 / 3.00 ( 2739) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4678 Ramachandran restraints generated. 2339 Oldfield, 0 Emsley, 2339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 128 ASP cc_start: 0.7505 (t0) cc_final: 0.7180 (t0) REVERT: A 16 MET cc_start: 0.7573 (mmt) cc_final: 0.7020 (mtp) REVERT: A 55 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8005 (tp) REVERT: A 104 GLU cc_start: 0.8402 (tp30) cc_final: 0.8095 (tp30) REVERT: A 271 MET cc_start: 0.8751 (mmm) cc_final: 0.7941 (ttm) REVERT: B 207 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8674 (t80) REVERT: B 368 CYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8303 (m) REVERT: C 100 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8664 (tt) REVERT: C 326 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7797 (mtp85) REVERT: F 70 HIS cc_start: 0.3510 (t70) cc_final: 0.2555 (t-170) REVERT: F 97 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7372 (m-80) REVERT: F 231 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7334 (ttp-110) REVERT: D 106 GLN cc_start: 0.8680 (tp40) cc_final: 0.8452 (tt0) REVERT: D 383 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.6499 (t80) outliers start: 54 outliers final: 44 residues processed: 203 average time/residue: 0.0994 time to fit residues: 33.4267 Evaluate side-chains 205 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 153 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 254 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain B residue 10 SER Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 108 HIS Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 368 CYS Chi-restraints excluded: chain C residue 12 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 35 LEU Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 326 ARG Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain F residue 40 LEU Chi-restraints excluded: chain F residue 97 PHE Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 200 LEU Chi-restraints excluded: chain F residue 231 ARG Chi-restraints excluded: chain F residue 343 VAL Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 207 PHE Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 277 ASP Chi-restraints excluded: chain D residue 280 PHE Chi-restraints excluded: chain D residue 310 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 383 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 138 optimal weight: 0.7980 chunk 183 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 0.3980 chunk 154 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 106 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS F 226 HIS ** D 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 HIS D 137 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.158303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.117601 restraints weight = 26130.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116040 restraints weight = 40314.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.117648 restraints weight = 34705.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.118427 restraints weight = 20033.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.119413 restraints weight = 17317.199| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17944 Z= 0.157 Angle : 0.605 13.497 24385 Z= 0.289 Chirality : 0.042 0.155 2845 Planarity : 0.005 0.058 3175 Dihedral : 3.783 55.287 2503 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.47 % Allowed : 28.47 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 2339 helix: 2.30 (0.18), residues: 896 sheet: 0.02 (0.20), residues: 698 loop : -0.94 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 323 TYR 0.010 0.001 TYR A 177 PHE 0.016 0.002 PHE D 280 TRP 0.033 0.001 TRP A 43 HIS 0.013 0.001 HIS D 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (17944) covalent geometry : angle 0.60491 / 0.29 (24385) hydrogen bonds : bond 0.03600 / 2.49 ( 921) hydrogen bonds : angle 4.32869 / 3.08 ( 2739) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.68 seconds wall clock time: 43 minutes 39.81 seconds (2619.81 seconds total)